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JAK2_HUMAN_536_835_ATPsite

Tyrosine-protein kinase JAK2 [Protein kinase superfamily. Tyr protein kinase family. JAK subfamily]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (JAK2_HUMAN):D: Protein kinase 1 (551:555, 557, 559, 579, 581, 610, 626:633, 635, 636, 640, 673, 677, 678, 680, 698, 700, 701)551:555, 557, 559, 579, 581, 610, 626:633, 635, 636, 640, 673, 677, 678, 680, 698, 700, 701

Full PDB list

4fvp, 4fvq, 4fvr, 5i4n, 5usz, 5ut0, 5ut1, 5ut2, 5ut3, 5ut4, 5ut5, 5ut6 (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
L
5
5
1
G
5
5
2
Q
5
5
3
G
5
5
4
T
5
5
5
T
5
5
7
I
5
5
9
L
5
7
9
K
5
8
1
V
6
1
0
Q
6
2
6
E
6
2
7
F
6
2
8
V
6
2
9
K
6
3
0
F
6
3
1
G
6
3
2
S
6
3
3
T
6
3
6
N
6
7
3
K
6
7
7
N
6
7
8
L
6
8
0
S
6
9
8
[1]4fvp.a none . . . . . . . . . . . . . . . . . . . . . . . .
[1]5i4n.a atp,mg32 . . . . . . . . . . . . . . . . . . . . . . . .
[1]5usz.a ske27 . . . . . . . . . . . . . . . . . . . . . . . .
[1]5ut0.a 35r28 . . . . . . . . . . . . . . . . . . . . . . . .
[1]5ut1.a 7dz24 . . . . . . . . . . . . . . . . . . . . . . . .
[1]5ut2.a 3yt29 . . . . . . . . . . . . . . . . . . . . . . . .
[1]5ut3.a ik118 . . . . . . . . . . . . . . . . . . . . . . . .
[1]5ut4.a dqx36 . . . . . . . . . . . . . . . . . . . . . . . .
[1]5ut5.a 2hb30 . . . . . . . . . . . . . . . . . . . . . . . .
[1]5ut6.a 8my23 . . . . . . . . . . . . . . . . . . . . . . . .

Legend

B backbone contact  S side chain contact  F BB + SCh
.
 no contact C covalent bond
X mutation to X * complex cases - deletion
M contact with cofactors/metals (if any)

Site contact map

[download in TSV format]
   
PDB.ch
A1
L
5
5
1
G
5
5
2
Q
5
5
3
G
5
5
4
T
5
5
5
T
5
5
7
I
5
5
9
L
5
7
9
K
5
8
1
V
6
1
0
Q
6
2
6
E
6
2
7
F
6
2
8
V
6
2
9
K
6
3
0
F
6
3
1
G
6
3
2
S
6
3
3
D
6
3
5
T
6
3
6
K
6
4
0
N
6
7
3
K
6
7
7
N
6
7
8
L
6
8
0
S
6
9
8
P
7
0
0
G
7
0
1
[1]4fvp.a . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5i4n.a . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5usz.a . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5ut0.a . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5ut1.a . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5ut2.a . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5ut3.a . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5ut4.a . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5ut5.a . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5ut6.a . . . . . . . . . . * . . . . . . . . . . . * . . . . .

Legend

B backbone contact  S side chain contact  F BB + SCh
.
 no contact C covalent bond
X X X X X  clash
X mutation to X * complex cases - deletion
M contact with cofactors/metals (if any)

Pocket-ligand steric compatibility

Ligands (x) vs pockets (y) colored by number of steric clashes

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pocketligand
≥10
9
8
7
6
5
4
3
2
1
0
4fvp.a is apo
5i4n.a:atp,mg
5usz.a:ske
5ut0.a:35r
5ut1.a:7dz
5ut2.a:3yt
5ut3.a:ik1
5ut4.a:dqx
5ut5.a:2hb
5ut6.a:8my
[1] 4fvp.a
-
0.6 0.2 0.1 0.6 0.3 0.1 0.8 0.7 0.2
[1] 5i4n.a -
0.1
0.3 0.1 0.7 0.2 0.3 0.3 0.6 0.5
[1] 5usz.a - 0.4
0
0.1 0.3 0.6 0.1 0.2 0.3 0.1
[1] 5ut0.a - 0.5 0.2
0
0.3 0.6 0 0.3 0.3 0.1
[1] 5ut1.a - 0.8 0.1 0.1
0.1
0.3 0 0.3 0.4 0.1
[1] 5ut2.a - 0.2 0.1 0 0.1
0
0.1 0.2 0.2 0.1
[1] 5ut3.a - 0.3 0.2 0 0.2 0.6
0
0.5 0.3 0.2
[1] 5ut4.a - 0.2 0 0 0.1 0.1 0.1
0
0.1 0.2
[1] 5ut5.a - 0.7 0 0 0.1 0.6 0.1 0.1
0
0.3
[1] 5ut6.a - 1.2 0.5 0 0.7 0.7 0 1.1 1.0
0
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (1 cluster)

Pockets (x) vs pockets (y) colored by ligand clash profile difference

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pocketpocket
≥1.
.9
.8
.7
.6
.5
.4
.3
.2
.1
.0
4fvp.a
5i4n.a
5usz.a
5ut0.a
5ut1.a
5ut2.a
5ut3.a
5ut4.a
5ut5.a
5ut6.a
[1] 4fvp.a
0
.06 .06 .06 .03 .05 .05 .05 .06 .06
[1] 5i4n.a .06
0
.06 .07 .07 .05 .06 .04 .06 .09
[1] 5usz.a .06 .06
0
.05 .05 .03 .03 .03 .04 .08
[1] 5ut0.a .06 .07 .05
0
.04 .04 .03 .04 .07 .09
[1] 5ut1.a .03 .07 .05 .04
0
.04 .05 .04 .05 .09
[1] 5ut2.a .05 .05 .03 .04 .04
0
.03 .01 .05 .10
[1] 5ut3.a .05 .06 .03 .03 .05 .03
0
.04 .05 .08
[1] 5ut4.a .05 .04 .03 .04 .04 .01 .04
0
.04 .10
[1] 5ut5.a .06 .06 .04 .07 .05 .05 .05 .04
0
.09
[1] 5ut6.a .06 .09 .08 .09 .09 .10 .08 .10 .09
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.6 Å)

Pockets (x) vs pockets (y) colored by RMSD of site residue backbone atoms

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pocketpocket
≥10 Å
9 Å
8 Å
7 Å
6 Å
5 Å
4 Å
3 Å
2 Å
1 Å
0 Å
4fvp.a
5i4n.a
5usz.a
5ut0.a
5ut1.a
5ut2.a
5ut3.a
5ut4.a
5ut5.a
5ut6.a
[1] 4fvp.a
0
0.8 0.4 0.4 0.3 0.4 0.3 0.5 0.5 0.4
[1] 5i4n.a 0.8
0
0.8 1.1 0.9 0.7 1.0 0.8 0.8 1.0
[1] 5usz.a 0.4 0.8
0
0.5 0.5 0.3 0.5 0.2 0.2 0.6
[1] 5ut0.a 0.4 1.1 0.5
0
0.3 0.6 0.2 0.5 0.6 0.2
[1] 5ut1.a 0.3 0.9 0.5 0.3
0
0.4 0.2 0.4 0.5 0.3
[1] 5ut2.a 0.4 0.7 0.3 0.6 0.4
0
0.5 0.3 0.4 0.6
[1] 5ut3.a 0.3 1.0 0.5 0.2 0.2 0.5
0
0.5 0.5 0.2
[1] 5ut4.a 0.5 0.8 0.2 0.5 0.4 0.3 0.5
0
0.2 0.5
[1] 5ut5.a 0.5 0.8 0.2 0.6 0.5 0.4 0.5 0.2
0
0.6
[1] 5ut6.a 0.4 1.0 0.6 0.2 0.3 0.6 0.2 0.5 0.6
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.4 Å)

Pockets (x) vs pockets (y) colored by RMSD of all site residue atoms

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pocketpocket
≥10 Å
9 Å
8 Å
7 Å
6 Å
5 Å
4 Å
3 Å
2 Å
1 Å
0 Å
4fvp.a
5i4n.a
5usz.a
5ut0.a
5ut1.a
5ut2.a
5ut3.a
5ut4.a
5ut5.a
5ut6.a
[1] 4fvp.a
0
1.1 0.6 0.6 0.4 0.5 0.6 0.7 0.9 0.6
[1] 5i4n.a 1.1
0
0.9 1.2 1.2 1.1 1.1 1.0 1.0 1.2
[1] 5usz.a 0.6 0.9
0
0.7 0.6 0.5 0.6 0.4 0.5 0.6
[1] 5ut0.a 0.6 1.2 0.7
0
0.5 0.7 0.3 0.6 0.7 0.5
[1] 5ut1.a 0.4 1.2 0.6 0.5
0
0.4 0.5 0.6 0.9 0.6
[1] 5ut2.a 0.5 1.1 0.5 0.7 0.4
0
0.6 0.5 0.7 0.7
[1] 5ut3.a 0.6 1.1 0.6 0.3 0.5 0.6
0
0.6 0.7 0.4
[1] 5ut4.a 0.7 1.0 0.4 0.6 0.6 0.5 0.6
0
0.4 0.7
[1] 5ut5.a 0.9 1.0 0.5 0.7 0.9 0.7 0.7 0.4
0
0.9
[1] 5ut6.a 0.6 1.2 0.6 0.5 0.6 0.7 0.4 0.7 0.9
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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